proteomics

Viewing posts tagged proteomics

09 Feb 2022

Study reveals the protein machinery central to CoQ trafficking in yeast

By nickwiecien

Beyond its role in mitochondrial bioenergetics, Coenzyme Q (CoQ, ubiquinone) serves as a key membrane-embedded antioxidant throughout the cell. However, how CoQ is moved from its site of synthesis on the inner mitochondrial membrane to other sites remains a longstanding mystery. In a recent study, researchers identified two highly conserved but poorly characterized mitochondrial proteins that affect this process. Their results reveal the protein machinery central to CoQ trafficking in yeast and lend insights into the broader interplay between mitochondria and the rest of the cell.

Read the article: UbiB proteins regulate cellular CoQ distribution in Saccharomyces cerevisiae

31 Jan 2022

New plasma protocol for LC-MS/MS

By nickwiecien

Evgenia Shishkova has developed a new protocol that offers step-by-step instructions for preparation of raw blood plasma for liquid chromatography – tandem mass spectrometry (LC-MS/MS). The technique is simple, robust, and reproducible. The entire transformation only takes 3–4 h. This protocol can be adopted for large-scale studies and automation.

Process is available in STAR Protocols: Rapid preparation of human blood plasma for bottom-up proteomics analysis

27 Oct 2021

New study asks “Do oral diseases correlate with other health outcomes?”

By nickwiecien

The human mouth harbors a wide variety of microbes – over 700 kinds. These bacteria are in saliva, on the tongue and cheeks, on the tooth surface and under the gums. The development of plaque is particularly important in diseases like tooth decay and gum disease. The oral microbiota that contribute to these disease are also correlated with other diseases, including diabetes, arthritis, and heart disease, suggesting they have a broad impact on human health. This study analyzed the microbiome, proteome, lipidome, and metabolome of dental plaque samples from individuals with periodontal disease and pre- and type 2 diabetes.

Read the article: Proteomics, lipidomics, metabolomics and 16S rDNA sequencing of dental plaque from patients with diabetes and periodontal disease.

Read the article: Proteomics, lipidomics, metabolomics and 16S rDNA sequencing of dental plaque from patients with diabetes and periodontal disease

07 Oct 2021

DiLeu tagging provides insight into human pancreas development

By nickwiecien

The extracellular matrix (ECM) is unique to each tissue, it guides cell differentiation, migration, morphology, and function. It has not been systematically studied in the human pancreas. In this paper, Li et al describe how they used mass spectrometry-based strategies using N,N-dimethyl leucine isobaric tags to identify proteome-wide and ECM-specific alterations in four age groups. They found 3,523 proteins and quantified 117 of them. This work will contribute to understanding the critical roles ECM plays in human pancreas development and maturation.

Read the article: Proteome-wide and matrisome-specific alterations during human pancreas development and maturation

18 Aug 2021

Data suggest a unique inflammatory signature associated with severe COVID19

By nickwiecien

The COVID19 pandemic will cause more than a million of deaths worldwide, primarily due to complications from acute respiratory distress syndrome (ARDS). Controversy surrounds the current cytokine/chemokine profile of COVID19-associated ARDS, with some groups suggesting that it is similar to non-COVID19 ARDS patients and others observing substantial differences. Balnis et. al. conducted a study of 41 mechanically ventilated patients with COVID19 infection using highly calibrated methods to define the levels of plasma cytokines/chemokines. Plasma IL1RA and IL8 were found positively associated with mortality, while RANTES and EGF negatively associated with that outcome. However, the leukocyte gene expression of these proteins had no significant correlation with mortality. Their data suggest a unique inflammatory signature associated with severe COVID19.

Read the article: Unique inflammatory profile is associated with higher SARS-CoV-2 acute respiratory distress syndrome (ARDS) mortality

02 Aug 2021

Biologically relevant proteins in Alzheimer’s Disease

By nickwiecien

Proteomic analysis of cerebrospinal fluid (CSF) holds great promise in understanding the progression of neurodegenerative diseases, including Alzheimer’s disease (AD). As one of the primary reservoirs of neuronal biomolecules, CSF provides a window into the biochemical and cellular aspects of the neurological environment. Using mass spectrometry technologies, McKetney et. al. quantified 700 proteins across 10 pairs of age- and sex-matched participants. Using the paired structure, they identified a small group of biologically relevant proteins that show substantial changes in abundance between normal and AD participants. These findings suggest the utility of fractionating a single sample and using matching to increase proteomic depth in CSF.

Read the article: Pilot Proteomic Analysis of Cerebrospinal Fluid in Alzheimer’s Disease. Proteomics Clinical Applications.

17 Mar 2021

Achieving a simplified, multi-omics workflow

By nickwiecien

An article by Yuchen He et. al. titled “Multi-omic Single-Shot Technology for Integrated Proteome and Lipidome Analysis” was recently published as one of the cover stories in Analytical Chemistry.

This article describes a technology to achieve broad and deep coverage of multiple molecular classes simultaneously through Multi-omics (proteome, lipidome, and metabolome) single-shot technology (MOST), requiring only one column, one LC-MS instrument, and a simplified workflow.

10 Mar 2021

Adding FAIMS to the phosphoproteomic workflow

By nickwiecien

Mass spectrometry is the premier tool for identifying and quantifying protein phosphorylation on a global scale. Analysis of phosphopeptides requires enrichment, and even after the samples remain highly complex and exhibit a broad dynamic range of abundance. A recent publication by Muehlbauer et. al. found that incorporating a commercialized aerodynamic high-field asymmetric waveform ion mobility spectrometry (FAIMS) device into the phosphoproteomic workflow was a valuable addition with greater benefits emerging from longer analyses and higher amounts of material.

Read the article, Global Phosphoproteome Analysis Using High-Field Asymmetric Waveform Ion Mobility Spectrometry on a Hybrid Orbitrap Mass Spectrometer.

30 Dec 2020

Recent publication highlights phosphoproteome analysis using FAIMS

By nickwiecien

Mass spectrometry is the premier tool for identifying and quantifying protein phosphorylation. Analysis of phosphopeptides requires enrichment, and even after that step, the samples remain highly complex and exhibit broad dynamic range of abundance. In a recent publication, Muehlbauer et al. describe a method for integrating a high-field asymmetric waveform ion mobility spectrometry (FAIMS) device into the workflow. The data collected with FAIMS yielded a 26% increase in total reproducible measurements, leading researchers to conclude that the new FAIMS technology is a valuable addition to any phosphoproteomic workflow, with greater benefits emerging from longer analyses and higher amounts of material.

Read the publication here: Global Phosphoproteome Analysis Using High-Field Asymmetric Waveform Ion Mobility Spectrometry on a Hybrid Orbitrap Mass Spectrometer

16 Dec 2020

Relish protein level affects secondary traumatic brain injuries

By nickwiecien

Brain trauma is caused by both primary and secondary injuries. Primary injuries result from the physical damage to the brain, and secondary injuries from the bodies’ responses to those injuries. A recent publication in Genetics by Swanson et al. describes using mass spectrometry to investigate secondary injuries in the Relish (Rel) protein level in fly heads after a primary brain injury. They found changes in Rel levels were necessary for secondary traumatic brain injuries to occur.

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